On the design of a molecular dynamics based model for studying receptor-receptor interactions: Systems Biology, Molecular Dynamics, and biomechanics

•Content

Introduction

•Methodological procedures

•Theoretical Background

•Receptors

•Dimerization and ligand binding

•Bioinformatics and mathematical modelling

•G-protein-coupled receptor dynamics

•The receptor–dimer cooperativity index

•Single-molecule imaging revealed dynamic GPCR dimerization

•Proposed model

•Conclusions and Final remarks

•References 

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Introduction

The pharmaceutical industries is likely to be amongst the most important and controversy ones. Issues present on the industries vary from misuse of advances such as not allowing drugs to reach the consumers or even manipulation of results. However, with no doubt , this is an extreme active area. Hot topics at the moment are: Systems Biology, Systems (bio) Medicine, P4 Medicine, and Systems Pharmacology.

The several scale to studying matter, from a physics viewpoint and from a biological viewpoint. For physics what matters is size rather organization. For physics the brain and a stone of the same size and mass is the same thing, but for biology one is a miracle of life and the second is a chunk of matter, useless.

 

The several levels of organization from human to genes, each level can be homeland for modeling, approaches that mixture them are in general called multiscales approaches

Scheme depicting the importance of receptors. A distal region can be controlled due to the concept of ligand and receptors



scheme for the methodology proposed for developing the software. the sphere supposes to represent the cell surface, whereas the dots are the dimers, or even monomers, that is, any clusters that can be considered a point, a node.

Videos used on the talk

  

This video was produced in 2012 in Gdansk as a warming up exercise in Continuous and Discrete simulations, taught by prof. Sergey Kshevetskii
Theoretical Physics Department of Immanuel Kant Russian
State University. The model is simple, just several particles in a box, with a potential between them, they are given an initial kick, there is no dissipation. 

This video was produced in Gdansk, as part of the lesson in classical simulations, by Winczewski Szymon, see Necking (nanowire)